clusterStats: Derive summary statistics for clusters

In MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

Description

A function that derives summary statistics for clusters.

Usage

clusterStats(fcsFrame, clusterList, fcsNames)

Arguments

fcsFrame	A flow Frame object returned from preprocessing function. Must contain a parameter called "sample_id" that specify the origin of each cell using integer IDs.
clusterList	A list, each element should be a vector containing the IDs of all cells that belong to a cluster.
fcsNames	A vector of fcs file names. Each element corresponds to an integer ID in the "sample_id" parameter in fcsFrame.

Value

Returns a data frame, rows correspond to each fcs file, columns correspond to MFI of markers or fractions.

Examples

# Find fcs files
files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
                  package="MetaCyto")
files=list.files(files,pattern="fcs$",full.names=TRUE)
# Preprocess
fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
# Search clusters
cluster_list=searchCluster(fcsFrame=fcs,
                           clusterLabel=c("CD3+|CD8+","CD3-|CD19+"))
# derive summary statistics
cluster_stats=clusterStats(fcsFrame=fcs,
                           clusterList=cluster_list$clusterList,
                           fcsNames=files)

MetaCyto documentation built on Nov. 8, 2020, 7:50 p.m.